Substituted anthraquinones represent a potential scaffold for DNA methyltransferase 1-specific inhibitors

A review on recent advances in assays for DNMT1: a promising diagnostic biomarker for multiple human cancers

The abnormal expression of human DNA methyltransferases (DNMTs) is closely related with the occurrence and development of a wide range of human cancers. DNA (cytosine-5)-methyltransferase-1 (DNMT1) is the most abundant human DNA methyltransferase and is mainly responsible for genomic DNA methylation patterns. Abnormal expression of DNMT1 has been found in many kinds of tumors, and DNMT1 has become a valuable target for the diagnosis and drug therapy of diseases. Nowadays, DNMT1 has been found to be involved in multiple cancers such as pancreatic cancer, breast cancer, bladder cancer, lung cancer, gastric cancer and other cancers. In order to achieve early diagnosis and for scientific research, various analytical methods have been developed for qualitative or quantitative detection of low-abundance DNMT1 in biological samples and human tumor cells. Herein, we provide a brief explication of the research progress of DNMT1 involved in various cancer types. In addition, this review focuses on the types, principles, and applications of DNMT1 detection methods, and discusses the challenges and potential future directions of DNMT1 detection.

A pan-cancer analysis of Dyskeratosis congenita 1 (DKC1) as a prognostic biomarker

BACKGROUND

Dyskeratosis congenita 1 (DKC1), a critical component of telomerase complex, is highly expressed in a variety of human cancers. However, the association of DKC1 with cancer occurrence and development stages is not clear, making a pan-cancer analysis crucial.

METHODS

We conducted a study using various bioinformatic databases such as TIMER, GEPIA, UALCAN, and KM plotter Analysis to examine the different expressions of DKC1 in multiple tissues and its correlation with pathological stages. Through KEGG analysis, GO enrichment analysis and Venn analysis, we were able to reveal DKC1-associated genes and signaling pathways. In addition, we performed several tests including the CCK, wound healing assay, cell cycle arrest assay, transwell assay and Sa-β-gal staining on DKC1-deleted MDA-231 cells.

RESULTS

Our study demonstrates that DKC1 has relatively low expression specificity in different tissues. Furthermore, we found that in ACC, KICH, KIRP and LIHC, the expression level of DKC1 is positively correlated with pathological stages. Conversely, in NHSC, KIRP, LGG, LIHC, MESO and SARC, we observed a negative influence of DKC1 expression level on the overall survival rate. We also found a significant positive correlation between DKC1 expression and Tumor Mutational Burden in 14 tumors. Additionally, we observed a significantly negative impact of DKC1 DNA methylation on gene expression at the promoter region in BRCA. We also identified numerous phosphorylation sites concentrated at the C-terminus of the DKC1 protein. Our GO analysis revealed a correlation between DKC1 and ribosomal biosynthesis pathways, and the common element UTP14A was identified. We also observed decreased rates of cell proliferation, migration and invasion abilities in DKC1-knockout MDA-MB-231 cell lines. Furthermore, DKC1-knockout induced cell cycle arrest and caused cell senescence.

CONCLUSIONS

Our findings suggest that the precise expression of DKC1 is closely associated with the occurrence and developmental stages of cancer in multiple tissues. Depletion of DKC1 can inhibit the abilities of cancer cells to proliferate, migrate, and invade by arresting the cell cycle and inducing cell senescence. Therefore, DKC1 may be a valuable prognostic biomarker for the diagnosis and treatment of cancer in various tissues.

Disease-Associated Mutation A554V Disrupts Normal Autoinhibition of DNMT1

DNA methyltransferase 1 (DNMT1) is the enzyme primarily responsible for propagation of the methylation pattern in cells. Mutations in DNMT1 have been linked to the development of adult-onset neurodegenerative disorders; these disease-associated mutations occur in the regulatory replication foci-targeting sequence (RFTS) domain of the protein. The RFTS domain is an endogenous inhibitor of DNMT1 activity that binds to the active site and prevents DNA binding. Here, we examine the impact of the disease-associated mutation A554V on normal RFTS-mediated inhibition of DNMT1. Wild-type and mutant proteins were expressed and purified to homogeneity for biochemical characterization. The mutation increased DNA binding affinity ~8-fold. In addition, the mutant enzyme exhibited increased DNA methylation activity. Circular dichroism (CD) spectroscopy revealed that the mutation does not significantly impact the secondary structure or relative thermal stability of the isolated RFTS domain. However, the mutation resulted in changes in the CD spectrum in the context of the larger protein; a decrease in relative thermal stability was also observed. Collectively, this evidence suggests that A554V disrupts normal RFTS-mediated autoinhibition of DNMT1, resulting in a hyperactive mutant enzyme. While the disease-associated mutation does not significantly impact the isolated RFTS domain, the mutation results in a weakening of the interdomain stabilizing interactions generating a more open, active conformation of DNMT1. Hyperactive mutant DNMT1 could be responsible for the increased DNA methylation observed in affected individuals.

Reversal of Epigenetic Peroxisome Proliferator-Activated Receptor-γ Suppression by Diacerein Alleviates Oxidative Stress and Osteoarthritis in Mice

Aims: The pathogenesis of osteoarthritis (OA) is characterized by oxidative stress (OS) and sustained inflammation that are substantially associated with epigenetic DNA methylation alterations of osteogenic gene expression. Diacerein as an anthraquinone anti-OA drug exhibits multiple chondroprotective properties, but less clarified pharmacological actions. Since anthraquinone contain an epigenetic modulating property, in this study we investigate whether the anti-OA functions of diacerein involve DNA methylation modulation and antioxidant signaling. Results: The OA mice incurred by destabilization of medial meniscus exhibited marked suppression of peroxisome proliferator-activated receptor-gamma (PPARγ), a chondroprotective transcription factor with anti-inflammation and OS-balancing properties, aberrant upregulations of DNA methyltransferase (DNMT)1/3a, and PPARγ promoter hypermethylation in knee joint cartilage. Diacerein treatment mitigated the cartilage damage and significantly inhibited the DNMT1/3a upregulation, the PPARγ promoter hypermethylation, and the PPARγ loss, and it effectively corrected the adverse expression of antioxidant enzymes and inflammatory cytokines. In cultured chondrocytes, diacerein reduced the interleukin-1β-induced PPARγ suppression and the abnormal expression of its downstream antioxidant enzymes in a gain of DNMT and PPARγ inhibition-sensitive manner, and in PPARγ knockout mice, the anti-OA effects of diacerein were significantly reduced. Innovation: Our work reveals a novel anti-OA pharmacological property of diacerein and identifies the aberrant DNMT elevation and the resultant PPARγ suppression as an important epigenetic pathway that mediates diacerein's anti-OA activities. Conclusion: DNA methylation aberration and the resultant PPARγ suppression contribute significantly to epigenetic OA pathogenesis, and targeting PPARγ suppression via DNA demethylation is an important component of diacerein's anti-OA functions. Antioxid. Redox Signal. 37, 40-53.

Epigenetic Modulators as Treatment Alternative to Diverse Types of Cancer

DNA is packaged in rolls in an octamer of histones forming a complex of DNA and proteins called chromatin. Chromatin as a structural matrix of a chromosome and its modifications are nowadays considered relevant aspects for regulating gene expression, which has become of high interest in understanding genetic mechanisms regulating various diseases, including cancer. In various types of cancer, the main modifications are found to be DNA methylation in the CpG dinucleotide as a silencing mechanism in transcription, post-translational histone modifications such as acetylation, methylation and others that affect the chromatin structure, the ATP-dependent chromatin remodeling and miRNA-mediated gene silencing. In this review we analyze the main alterations in gene expression, the epigenetic modification patterns that cancer cells present, as well as the main modulators and inhibitors of each epigenetic mechanism and the molecular evolution of the most representative inhibitors, which have opened a promising future in the study of HAT, HDAC, non-glycoside DNMT inhibitors and domain inhibitors.

Thiophene-2-carboxamide derivatives of anthraquinone: A new potent antitumor chemotype

The anthraquinone scaffold has long been known as a source of efficacious antitumor drugs. In particular, the various chemical modifications of the side chains in this scaffold have yielded the compounds potent for the wild type tumor cells, their counterparts with molecular determinants of altered drug response, as well as in vivo settings. Further exploring the chemotype of anticancer heteroarene-fused anthraquinones, we herein demonstrate that derivative of anthra[2,3-b]thiophene-2-carboxamide, (compound 8) is highly potent against a panel of human tumor cell lines and their drug resistant variants. Treatment with submicromolar or low micromolar concentrations of 8 for only 30 min was sufficient to trigger lethal damage of K562 chronic myelogenous leukemia cells. Compound 8 (2.5 μM, 3-6 h) induced an apoptotic cell death as determined by concomitant activation of caspases 3 and 9, cleavage of poly(ADP-ribose) polymerase, increase of Annexin V/propidium iodide double stained cells, DNA fragmentation (subG1 fraction) and a decrease of mitochondrial membrane potential. Neither a significant interaction with double stranded DNA nor strong inhibition of the DNA dependent enzyme topoisomerase 1 by 8 were detectable in cell free systems. Laser scanning confocal microscopy revealed that some amount of 8 was detectable in mitochondria as early as 5 min after the addition to the cells; exposure for 1 h caused significant morphological changes and clustering of mitochondria. The bioisosteric analog 2 in which the thiophene ring was replaced with furan was less active although the patterns of cytotoxicity of both derivatives were similar. These results point at the specific role of the sulfur atom in the antitumor properties of carboxamide derivatives of heteroarene-fused anthraquinone.

Disease-Associated Mutations G589A and V590F Relieve Replication Focus Targeting Sequence-Mediated Autoinhibition of DNA Methyltransferase 1

In eukaryotes, the most common epigenetic DNA modification is methylation of carbon 5 of cytosines, predominantly in CpG dinucleotides. Methylation patterns are established and maintained by a family of proteins known as DNA methyltransferases (DNMTs). DNA methylation is an important epigenetic mark associated with gene repression, and disruption of the normal DNA methylation pattern is known to play a role in several disease states. Methylation patterns are primarily maintained by DNMT1, which possesses specificity for methylation of hemimethylated DNA. DNMT1 is a multidomain protein with a C-terminal catalytic methyltransferase domain and a large N-terminal regulatory region. The replication focus targeting sequence (RFTS) domain, found in the regulatory region, is an endogenous inhibitor of DNMT1 activity. Recently, several mutations in the RFTS domain were shown to be causal for two adult onset neurodegenerative diseases; however, little is known about the impact of these mutations on the structure and function of DNMT1. Two of these mutations, G589A and V590F, are associated with development of autosomal dominant cerebellar ataxia, deafness, and narcolepsy (ADCA-DN). We have successfully expressed and purified G589A and V590F DNMT1 for in vitro studies. The mutations significantly decrease the thermal stability of DNMT1, yet the mutant proteins exhibit 2.5-3.5-fold increases in DNA binding affinity. In addition, the mutations weaken RFTS-mediated inhibition of DNA methylation activity. Taken together, these data suggest these disease-associated mutations decrease protein stability and, at least partially, relieve normal RFTS-mediated autoinhibition of DNMT1.